Contacts of the helix formed by residues 362 - 383 (chain A) in PDB entry 1YHV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A CYS 3.8 1.4 + - - +
361A MET* 1.3 76.1 - - - +
363A GLU* 1.3 64.0 + - - +
364A GLY* 2.9 8.1 + - - -
365A GLN* 2.9 44.4 + - - +
366A ILE* 3.0 21.9 + - - +
525A LYS* 2.7 29.1 + - - -
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Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A ASP* 1.3 74.6 - - - +
364A GLY* 1.3 57.0 - - - +
366A ILE* 3.4 9.8 + - + +
367A ALA* 2.9 31.4 + - - +
489A LYS 4.3 2.9 - - - +
490A LEU* 3.5 14.0 - - + +
491A SER* 2.7 49.2 + - - -
494A PHE* 3.5 27.2 - - + +
520A PHE* 3.9 8.1 - - + -
523A ILE* 3.9 16.8 - - + +
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Residues in contact with GLY 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A ASP* 2.9 8.5 + - - -
363A GLU* 1.3 77.7 - - - +
365A GLN* 1.3 60.8 + - - +
368A ALA* 3.2 13.7 + - - +
523A ILE* 3.6 24.3 - - - +
524A ALA* 3.4 2.4 - - - -
525A LYS* 3.0 37.0 + - - +
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Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A CYS 4.3 2.4 - - - +
361A MET* 3.6 22.0 - - + +
362A ASP* 2.9 51.3 + - - +
364A GLY* 1.3 76.5 - - - +
366A ILE* 1.3 64.1 + - - +
368A ALA* 3.3 7.1 + - - +
369A VAL* 3.2 19.8 + - - +
525A LYS* 4.3 5.0 - - + +
529A SER* 2.9 41.5 + - - +
530A LEU* 3.7 16.0 - - + +
532A PRO* 5.6 0.8 - - - +
533A LEU* 3.6 25.5 - - - +
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Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A MET* 3.7 29.8 - - + +
362A ASP 3.0 21.9 + - - +
363A GLU* 3.4 7.6 + - + +
365A GLN* 1.3 74.1 - - - +
367A ALA* 1.3 60.9 + - - +
369A VAL* 3.2 2.6 + - - +
370A CYS* 2.9 35.3 + - - -
454A ALA* 5.1 1.3 - - + -
457A MET* 3.9 49.6 - - + +
458A ILE* 4.3 3.8 - - + -
494A PHE* 3.7 39.5 - - + -
520A PHE* 4.1 2.9 - - + -
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A GLU 2.9 18.4 + - - +
365A GLN 3.3 0.2 - - - -
366A ILE* 1.3 76.4 - - - +
368A ALA* 1.3 58.7 + - - +
370A CYS* 4.4 0.4 - - - -
371A ARG* 2.9 30.7 + - - +
520A PHE* 3.4 44.4 - - + +
521A LEU* 3.6 6.5 - - - +
523A ILE* 3.9 3.6 - - + -
524A ALA* 3.8 21.4 - - + +
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Residues in contact with ALA 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A GLY 3.2 9.2 + - - +
365A GLN* 3.5 11.2 - - - +
366A ILE 3.2 0.8 - - - -
367A ALA* 1.3 79.0 - - - +
369A VAL* 1.3 62.6 + - - +
371A ARG* 3.3 7.6 + - - +
372A GLU* 3.0 29.7 + - - +
524A ALA* 3.6 10.2 - - + +
525A LYS 3.6 24.2 - - - +
526A PRO 5.1 0.7 - - - +
527A LEU* 3.9 18.6 - - + -
529A SER* 5.3 0.4 - - - +
530A LEU* 4.9 5.4 - - + -
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Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A LEU* 4.0 24.5 - - + -
361A MET* 3.9 15.3 - - + -
365A GLN 3.2 12.6 + - - +
366A ILE 3.7 6.1 - - - +
368A ALA* 1.3 76.8 - - - +
370A CYS* 1.3 63.9 + - - +
372A GLU* 3.2 2.6 + - - +
373A CYS* 3.0 35.5 + - - -
395A ILE* 4.9 0.7 - - + -
397A LEU* 5.3 2.7 - - + -
403A VAL* 4.2 20.2 - - + -
453A MET* 6.0 0.2 - - - -
457A MET* 3.9 22.2 - - + -
530A LEU* 4.0 21.3 - - + -
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Residues in contact with CYS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ILE* 2.9 29.5 + - - +
367A ALA* 3.7 5.8 - - - +
369A VAL* 1.3 76.8 - - - +
371A ARG* 1.3 57.5 + - - +
373A CYS* 3.4 6.4 + - - +
374A LEU* 2.9 33.6 + - - +
450A LEU* 4.5 12.2 - - + +
454A ALA* 4.4 8.7 - - - -
457A MET* 3.7 20.9 - - - -
497A PHE* 4.0 27.1 - - + -
520A PHE* 4.3 2.7 - - + -
521A LEU* 4.0 13.5 - - + -
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Residues in contact with ARG 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ALA 2.9 18.5 + - - +
368A ALA* 3.6 6.6 + - - +
369A VAL 3.2 0.2 - - - -
370A CYS* 1.3 77.5 - - - +
372A GLU* 1.3 91.2 + - - +
374A LEU* 3.2 2.8 + - - +
375A GLN* 3.0 44.5 + - + +
516A LEU* 4.0 4.0 - - + +
521A LEU* 3.8 36.4 + - + +
524A ALA* 3.7 23.5 + - - +
525A LYS 4.9 4.0 + - - -
526A PRO* 6.0 0.4 - - - +
527A LEU* 4.0 23.2 - - - +
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Residues in contact with GLU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ASN* 2.8 40.1 + - - +
368A ALA 3.0 20.0 + - - +
369A VAL 3.2 1.5 + - - +
371A ARG* 1.3 107.1 + - - +
373A CYS* 1.3 62.3 + - - +
375A GLN* 3.2 18.9 + - - +
376A ALA* 3.3 16.5 + - - +
403A VAL* 3.6 25.1 + - + +
527A LEU* 3.8 34.0 - - + +
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Residues in contact with CYS 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A VAL* 3.0 35.2 + - - +
370A CYS 3.8 4.3 - - - +
372A GLU* 1.3 76.2 - - - +
374A LEU* 1.3 59.4 + - - +
376A ALA* 3.2 9.0 + - - +
377A LEU* 3.0 34.1 + - + +
390A ILE* 6.3 2.0 - - + -
395A ILE* 3.8 31.6 - - + -
403A VAL* 4.2 8.5 - - - -
405A LEU* 5.6 1.7 - - - +
450A LEU* 3.9 22.7 - - + -
453A MET* 5.0 3.6 - - - -
457A MET* 6.3 0.2 - - - -
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A CYS 2.9 20.5 + - - +
371A ARG 3.2 1.3 + - - +
373A CYS* 1.3 77.4 - - - +
375A GLN* 1.3 56.8 + - - +
377A LEU* 3.8 3.8 - - + +
378A GLU* 2.8 32.6 + - - +
447A ILE* 3.8 23.6 - - + -
450A LEU* 3.5 19.7 - - + -
497A PHE* 3.9 19.1 - - + -
512A ALA* 4.0 16.6 - - + +
515A LEU* 3.8 24.9 - - + +
516A LEU* 3.6 18.1 - - + +
521A LEU* 3.7 23.6 - - + -
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Residues in contact with GLN 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ASN* 4.6 3.1 + - - +
326A ASN* 2.8 29.9 - - - +
371A ARG* 3.0 41.5 + - - +
372A GLU* 3.2 23.8 + - - +
373A CYS 3.2 0.2 - - - -
374A LEU* 1.3 76.0 - - - +
376A ALA* 1.3 62.2 + - - +
378A GLU* 3.6 2.4 + - - +
379A PHE* 3.2 23.2 + - - +
516A LEU* 3.8 19.4 - - + +
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Residues in contact with ALA 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A ASN* 4.2 7.2 - - - -
326A ASN* 3.6 34.0 - - + +
327A ILE* 4.4 5.8 - - + -
372A GLU 3.3 4.4 + - - +
373A CYS* 3.2 11.3 + - - +
375A GLN* 1.3 80.7 - - - +
377A LEU* 1.3 58.3 + - - +
379A PHE* 3.3 3.9 + - - +
380A LEU* 2.9 34.1 + - - +
405A LEU* 4.2 21.3 - - + -
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A CYS* 3.0 20.4 + - + +
374A LEU* 3.3 5.6 + - + +
376A ALA* 1.3 74.7 - - - +
378A GLU* 1.3 67.0 + - - +
380A LEU* 4.5 8.1 - - + -
381A HIS* 2.8 35.6 + - + +
387A HIS* 4.8 0.4 - - + -
390A ILE* 4.0 23.6 - - + -
405A LEU* 4.4 10.1 - - + -
446A ASP* 3.9 47.6 - - + +
447A ILE* 4.1 16.2 - - + -
450A LEU* 4.5 17.3 - - + -
512A ALA* 4.0 10.5 - - + -
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LEU 2.8 11.7 + - - +
375A GLN* 4.0 3.7 - - - +
377A LEU* 1.3 73.2 - - - +
379A PHE* 1.3 58.4 + - - +
381A HIS* 4.1 1.5 - - - +
382A SER* 2.9 38.1 + - - -
512A ALA* 3.6 13.1 - - + +
513A LYS* 3.6 35.8 + - + +
516A LEU* 2.4 43.5 - - + +
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Residues in contact with PHE 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A GLU 5.2 0.7 - - - -
322A ASN* 3.4 44.2 - - + -
323A LYS 3.5 18.8 - - - -
324A ASN* 3.5 34.8 - - + +
327A ILE* 4.1 10.8 - - + -
375A GLN 3.2 11.8 + - - +
376A ALA 3.5 7.4 - - - +
377A LEU 3.2 0.2 - - - -
378A GLU* 1.3 80.2 - - - +
380A LEU* 1.3 64.8 + - + +
382A SER* 2.8 21.5 + - - -
383A ASN* 2.9 36.7 + - - +
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A VAL* 5.5 0.2 - - + -
322A ASN* 4.4 11.7 - - + -
327A ILE* 3.8 22.4 - - + -
376A ALA 2.9 20.7 + - - +
377A LEU* 3.9 7.2 - - + +
379A PHE* 1.3 84.8 - - + +
381A HIS* 1.3 60.3 - - + +
383A ASN* 2.9 16.2 + - - -
384A GLN 3.1 0.3 + - - -
385A VAL* 2.9 50.4 + - + +
387A HIS* 4.6 10.5 - - + +
405A LEU* 3.8 23.3 - - + -
408A PHE* 3.7 30.3 - - + -
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Residues in contact with HIS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A LEU* 2.8 35.4 + - + +
378A GLU* 4.1 3.6 - - - +
380A LEU* 1.3 70.7 - - + +
382A SER* 1.3 61.7 + - - +
383A ASN 3.0 5.4 - - - -
384A GLN* 3.1 18.4 + - - +
385A VAL 3.3 19.1 - - - +
386A ILE* 4.4 0.7 - - - -
414A ILE* 5.9 0.5 - - - +
443A PRO* 3.2 49.3 + - + +
444A LYS* 6.3 0.2 - - + -
446A ASP* 2.9 34.0 + - + +
447A ILE* 4.7 8.7 - - + +
512A ALA* 4.1 16.7 + - + +
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Residues in contact with SER 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 2.9 20.5 + - - -
379A PHE* 2.8 19.9 + - - -
381A HIS* 1.3 76.4 - - - +
383A ASN* 1.3 66.1 + - - +
384A GLN* 3.3 16.2 + - - +
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Residues in contact with ASN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ASN* 3.7 21.1 + - - +
379A PHE* 2.9 41.1 + - - +
380A LEU* 2.9 9.5 + - - +
382A SER* 1.3 88.6 + - - +
384A GLN* 1.3 75.7 + - - +
385A VAL* 3.4 8.8 + - + +
413A GLN* 5.3 3.1 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il